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SNARE-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Profilin-like [ 55769] (10)
Superfamily:   SNARE-like [ 64356] (4)
Families:   Synatpobrevin N-terminal domain [ 64357] (2)
  Sedlin (SEDL) [ 82767]
  Clathrin coat assembly domain [ 75521] (2)
  SRP alpha N-terminal domain-like [ 90019] (2)


Superfamily statistics
Genomes (500) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 11,835 12,400 11
Proteins 11,774 12,365 11


Functional annotation
General category General
Detailed category Protein interaction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.065090.01374Least InformativeInherited
Biological Process (BP)biological regulation0.86751Least InformativeInherited
Biological Process (BP)cellular localization0.000025180Moderately InformativeDirect
Biological Process (BP)cell communication0.24681Moderately InformativeInherited
Biological Process (BP)single-organism transport11Moderately InformativeInherited
Biological Process (BP)macromolecule localization0.44130.07939Moderately InformativeInherited
Biological Process (BP)organic substance transport11Moderately InformativeInherited
Biological Process (BP)regulation of biological quality0.083250.8482Moderately InformativeInherited
Biological Process (BP)regulation of localization0.41590.4008Moderately InformativeInherited
Biological Process (BP)signaling0.16481Moderately InformativeInherited
Biological Process (BP)organelle organization0.29710.0000401Moderately InformativeInherited
Biological Process (BP)vesicle-mediated transport0.00000000005760InformativeDirect
Biological Process (BP)secretion0.0065370.00001998InformativeInherited
Biological Process (BP)single-organism intracellular transport0.1510.07729InformativeInherited
Biological Process (BP)regulation of neurotransmitter levels0.0000010.0000001642Highly InformativeDirect
Biological Process (BP)regulation of lipid storage0.0000087630.00000004662Highly InformativeDirect
Biological Process (BP)vesicle organization0.0000000049320Highly InformativeDirect
Biological Process (BP)Golgi vesicle transport0.000000042660Highly InformativeDirect
Biological Process (BP)vesicle localization0.000000000026910.000000000003443Highly InformativeDirect
Biological Process (BP)synaptic signaling0.00000036220.008073Highly InformativeInherited
Biological Process (BP)signal release0.000000097120.0135Highly InformativeInherited
Biological Process (BP)endocytosis11Highly InformativeInherited
Biological Process (BP)establishment of organelle localization0.0010740.0000002013Highly InformativeInherited
Molecular Function (MF)binding0.53791Least InformativeInherited
Molecular Function (MF)protein binding0.024670.2278Moderately InformativeInherited
Molecular Function (MF)transporter activity0.04780.05937Moderately InformativeInherited
Molecular Function (MF)molecular function regulator0.20990.5019Moderately InformativeInherited
Molecular Function (MF)guanyl-nucleotide exchange factor activity0.00019170.000628Highly InformativeDirect
Molecular Function (MF)protein transporter activity0.0000000027680.0000000000002233Highly InformativeDirect
Cellular Component (CC)membrane0.00000091980Least InformativeDirect
Cellular Component (CC)protein complex00Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.016290.00002474Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.083230Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.11270.04064Least InformativeInherited
Cellular Component (CC)organelle membrane0.0000000023510Moderately InformativeDirect
Cellular Component (CC)vesicle0.0000000017450Moderately InformativeDirect
Cellular Component (CC)membrane protein complex0.000000000000037790Moderately InformativeDirect
Cellular Component (CC)whole membrane00Moderately InformativeDirect
Cellular Component (CC)plasma membrane0.97511Moderately InformativeInherited
Cellular Component (CC)Golgi apparatus00InformativeDirect
Cellular Component (CC)transport vesicle0.0000045770.0000000006874InformativeDirect
Cellular Component (CC)cytoplasmic vesicle part00InformativeDirect
Cellular Component (CC)synapse0.0000030740.00004535InformativeDirect
Cellular Component (CC)endosome0.46880.1151InformativeInherited
Cellular Component (CC)plasma membrane protein complex0.0014270.01906InformativeInherited
Cellular Component (CC)secretory vesicle0.94231InformativeInherited
Cellular Component (CC)membrane region0.00024680.01135InformativeInherited
Cellular Component (CC)Golgi-associated vesicle00Highly InformativeDirect
Cellular Component (CC)synaptic vesicle0.000070290.00000004742Highly InformativeDirect
Cellular Component (CC)vesicle membrane00Highly InformativeDirect
Cellular Component (CC)coated vesicle00Highly InformativeDirect
Cellular Component (CC)tethering complex0.00000000051980.0000000000001655Highly InformativeDirect
Cellular Component (CC)endocytic vesicle0.72890.2746Highly InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular component organization or biogenesis 0.01374 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) organelle organization 0.0000401 Moderately Informative Direct
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) single-organism transport 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.07939 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.8482 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.4008 Moderately Informative Inherited
Biological Process (BP) signaling 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.4034 Moderately Informative Inherited
Biological Process (BP) microtubule-based process 0.00003813 Informative Direct
Biological Process (BP) vesicle-mediated transport 0 Informative Direct
Biological Process (BP) single-organism membrane organization 0.00000000002881 Informative Direct
Biological Process (BP) secretion 0.00001998 Informative Direct
Biological Process (BP) movement of cell or subcellular component 0.01674 Informative Inherited
Biological Process (BP) immune response 0.1146 Informative Inherited
Biological Process (BP) single-organism intracellular transport 0.07729 Informative Inherited
Biological Process (BP) regulation of neurotransmitter levels 0.0000001642 Highly Informative Direct
Biological Process (BP) myeloid leukocyte activation 0.000003795 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 0.00001294 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 0.00004101 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0.0000000001846 Highly Informative Direct
Biological Process (BP) regulation of lipid storage 0.00000004662 Highly Informative Direct
Biological Process (BP) vesicle organization 0 Highly Informative Direct
Biological Process (BP) endosomal transport 0.00002536 Highly Informative Direct
Biological Process (BP) single-organism membrane fusion 0.00000005035 Highly Informative Direct
Biological Process (BP) Golgi vesicle transport 0 Highly Informative Direct
Biological Process (BP) organelle fusion 0.00000000001404 Highly Informative Direct
Biological Process (BP) vesicle localization 0.000000000003443 Highly Informative Direct
Biological Process (BP) establishment of organelle localization 0.0000002013 Highly Informative Direct
Biological Process (BP) synaptic signaling 0.008073 Highly Informative Inherited
Biological Process (BP) signal release 0.0135 Highly Informative Inherited
Biological Process (BP) endocytosis 1 Highly Informative Inherited
Biological Process (BP) regulated exocytosis 1 Highly Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) protein binding 0.2278 Moderately Informative Inherited
Molecular Function (MF) transporter activity 0.05937 Moderately Informative Inherited
Molecular Function (MF) molecular function regulator 0.5019 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0.001871 Informative Inherited
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0.000628 Highly Informative Direct
Molecular Function (MF) protein transporter activity 0.0000000000002233 Highly Informative Direct
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) protein complex 0 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.00002474 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.04064 Least Informative Inherited
Cellular Component (CC) vacuole 0.0000005949 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 0.0000005517 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0 Moderately Informative Direct
Cellular Component (CC) membrane protein complex 0 Moderately Informative Direct
Cellular Component (CC) whole membrane 0 Moderately Informative Direct
Cellular Component (CC) plasma membrane 1 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum membrane 0.000008017 Informative Direct
Cellular Component (CC) Golgi apparatus 0 Informative Direct
Cellular Component (CC) transport vesicle 0.0000000006874 Informative Direct
Cellular Component (CC) organelle subcompartment 0.000000002692 Informative Direct
Cellular Component (CC) cytoplasmic vesicle part 0 Informative Direct
Cellular Component (CC) vacuolar part 0.00000003534 Informative Direct
Cellular Component (CC) synapse 0.00004535 Informative Direct
Cellular Component (CC) endosome 0.1151 Informative Inherited
Cellular Component (CC) plasma membrane protein complex 0.01906 Informative Inherited
Cellular Component (CC) secretory vesicle 1 Informative Inherited
Cellular Component (CC) membrane region 0.01135 Informative Inherited
Cellular Component (CC) lytic vacuole 0.01999 Informative Inherited
Cellular Component (CC) endoplasmic reticulum-Golgi intermediate compartment 0.00002401 Highly Informative Direct
Cellular Component (CC) Golgi-associated vesicle 0 Highly Informative Direct
Cellular Component (CC) synaptic vesicle 0.00000004742 Highly Informative Direct
Cellular Component (CC) vesicle membrane 0 Highly Informative Direct
Cellular Component (CC) coated vesicle 0 Highly Informative Direct
Cellular Component (CC) SNARE complex 0 Highly Informative Direct
Cellular Component (CC) tethering complex 0.0000000000001655 Highly Informative Direct
Cellular Component (CC) late endosome 0.1616 Highly Informative Inherited
Cellular Component (CC) endosome membrane 0.8388 Highly Informative Inherited
Cellular Component (CC) endocytic vesicle 0.2746 Highly Informative Inherited
Cellular Component (CC) lytic vacuole membrane 0.0107 Highly Informative Inherited

Document: GO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Congenital onset0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the face0.1566Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.7119Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal nasal morphology0.1425InformativeInherited
Phenotypic Abnormality (PA)Prominent nose0.0002555Highly InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell morphology variant0.000001837Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.000004228Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.00001492Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0000449Least InformativeDirect
Worm Phenotype (WP)cell development variant0.0001691Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.3921Least InformativeInherited
Worm Phenotype (WP)larval development variant0.3972Least InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant0.00000001262Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.0005803Moderately InformativeDirect
Worm Phenotype (WP)organism segment morphology variant0.004726Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.05497Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.07456Moderately InformativeInherited
Worm Phenotype (WP)nervous system morphology variant0.2256Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.4443Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.5875Moderately InformativeInherited
Worm Phenotype (WP)reproductive system development variant0.8139Moderately InformativeInherited
Worm Phenotype (WP)sick0.00009198InformativeDirect
Worm Phenotype (WP)sensillum morphology variant0.0002312InformativeDirect
Worm Phenotype (WP)diplotene progression during oogenesis variant0.0006354InformativeDirect
Worm Phenotype (WP)aldicarb response variant0.0009157InformativeDirect
Worm Phenotype (WP)pigmentation variant0.0028InformativeInherited
Worm Phenotype (WP)drug resistant0.002828InformativeInherited
Worm Phenotype (WP)gonad development variant0.004286InformativeInherited
Worm Phenotype (WP)body length variant0.005383InformativeInherited
Worm Phenotype (WP)mitosis variant0.007397InformativeInherited
Worm Phenotype (WP)body width variant0.00749InformativeInherited
Worm Phenotype (WP)organelle organization biogenesis variant0.07322InformativeInherited
Worm Phenotype (WP)alimentary system development variant0.08351InformativeInherited
Worm Phenotype (WP)meiotic chromosome organization variant0.1584InformativeInherited
Worm Phenotype (WP)gut granule development variant0.00001241Highly InformativeDirect
Worm Phenotype (WP)molt variant0.00003991Highly InformativeDirect
Worm Phenotype (WP)oocyte septum formation variant0.0000769Highly InformativeDirect
Worm Phenotype (WP)lysosome organization biogenesis variant0.0001218Highly InformativeDirect
Worm Phenotype (WP)dumpy0.0001694Highly InformativeDirect
Worm Phenotype (WP)clear0.0001766Highly InformativeDirect
Worm Phenotype (WP)chromosome condensation variant0.0002304Highly InformativeDirect
Worm Phenotype (WP)aldicarb resistant0.0003389Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)intracellular transport0.03053InformativeInherited
Yeast Phenotype (YP)protein transport0.004014Highly InformativeInherited

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)organism subdivision0Least InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)pollen tube cell0.00004486InformativeDirect
Plant structure DEvelopment stage (PDE)pollen development stage0.0001199Moderately InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processProtein transport0Moderately InformativeDirect
Biological processEndocytosis0InformativeDirect
Biological processER-Golgi transport0Highly InformativeDirect
Biological processExocytosis0.0000001645Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Cellular componentCell junction0.00286Moderately InformativeInherited
Cellular componentLysosome0.0000005109InformativeDirect
Cellular componentSynapse0.000002874InformativeDirect
Cellular componentCoated pit0Highly InformativeDirect
Cellular componentSynaptosome0.000008654Highly InformativeDirect
DomainTransmembrane0.000002706Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
Molecular functionLipid-binding0.000001609Moderately InformativeDirect
Post-translational modificationPhosphoprotein0.000002095Least InformativeDirect
Post-translational modificationAcetylation0.000005344Least InformativeDirect
Post-translational modificationPalmitate0.0000000000001455Moderately InformativeDirect
Post-translational modificationMethylation0.0000009708Moderately InformativeDirect
Post-translational modificationPrenylation0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011012 SSF64356 Protein matches
Abstract

VAMPs (and its homologue synaptobrevins) define a group of SNARE proteins that contain a C-terminal coiled-coil/SNARE motif, in combination with variable N-terminal domains that are used to classify VAMPs: those containing longin N-terminal domains (~150 aa) are referred to as longins, while those with shorter N-termini are referred to as brevins [PubMed12914952]. Longins are the only type of VAMP protein found in all eukaryotes, suggesting that their longin domain is essential. The longin domain is thought to exert a regulatory function. Longin domains have been shown to share the same structural fold, a profilin-like globular domain consisting of a five-stranded antiparallel beta-sheet that is sandwiched by an alpha-helix on one side, and two alpha-helices on the other (beta(2)-alpha-beta(3)-alpha(2)).

Other families have been shown to contain domains that structurally resemble the VAMP longin domain. An example is the eukaryotic conserved protein, SEDL, which is a component of the transport protein particle (TRAPP), critically involved in endoplasmic reticulum-to-Golgi vesicle transport; mutations in the SEDL gene are associated with an X-linked skeletal disorder, spondyloepiphyseal dysplasia tarda [PubMed12361953]. Another example is the assembly domain of clathrin coat proteins, such as Mu2 adaptin (AP50) and Sigma2 adaptin (AP17), which structurally resemble the longin domain. AP50 and AP17 are two of the proteins that make up the core of AP2, a complex that functions in clathrin-mediated endocytosis [PubMed12086608].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 7 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a SNARE-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 7 hidden Markov models representing the SNARE-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]